The income of a New York non-resident who never physically works in New York is not subject to New York taxation.
File NY Form 2104.1 with your employer:
https://www.tax.ny.gov/pdf/current_forms/it/it2104_1_fill_in.pdf
If NY taxes were incorrectly withheld, file a non-resident NY tax return on which you show the withholding, but allocate zero income to NY. This should result in a full refund.
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
